[gmx-users] problem with make_ndx

[Justin A. Lemkul]

Anushree Tripathi wrote:
> But in coordinate file(.pdb file) ,I am not getting the atoms which 
> belongs to DPPC.only I have included the name of dppc.itp file like this:

This is precisely the problem - you have no DPPC in the coordinate file.

> ;Include DPPC chain topology
> #include "dppc.itp"
> 

Adding information to the topology has no effect on the coordinate file.

Consult the membrane protein tutorial for how to properly build such a system.

http://www.gromacs.org/Documentation/Tutorials#Membrane_Simulations

-Justin

> That's why I have found the atoms wich belongs to DPPC molecule from 
> dppc.itp file itself.
> 
> 
> On Wed, Feb 1, 2012 at 12:40 PM, Mark Abraham <Mark.Abraham at anu.edu.au 
> <mailto:Mark.Abraham at anu.edu.au>> wrote:
> 
>     On 1/02/2012 6:04 PM, Anushree Tripathi wrote:
>>     When I run the command (i.e., make_ndx -f em.gro -o index.ndx) ,it
>>     is showing the following options:
>>      0 System              : 18379 atoms
>>       1 Protein             : 11739 atoms
>>       2 Protein-H           :  9135 atoms
>>       3 C-alpha             :  1173 atoms
>>       4 Backbone            :  3519 atoms
>>       5 MainChain           :  4693 atoms
>>       6 MainChain+Cb        :  5773 atoms
>>       7 MainChain+H         :  5842 atoms
>>       8 SideChain           :  5897 atoms
>>       9 SideChain-H         :  4442 atoms
>>      10 Prot-Masses         : 11739 atoms
>>      11 non-Protein         :  6640 atoms
>>      12 Water               :  6636 atoms
>>      13 SOL                 :  6636 atoms
>>      14 non-Water           : 11743 atoms
>>      15 Ion                 :     4 atoms
>>      16 CL                  :     4 atoms
>>      17 Water_and_ions      :  6640 atoms
> 
>     So your system has 18K atoms, with 11K protein and the rest solvent
>     and ions. As Justin suggested, this coordinate file does not have
>     DPPC in it.
> 
> 
> 
>>     for my work, I used 16|13 then 1|11.lastly I saved it using
>>     'q'.But there is no option for DPPC (as given in tutorial we have
>>     to merge protein with DPPC).After runing the command (grompp -f
>>     nvt.mdp -c em.gro -p topol.top -n index.ndx -o nvt.tpr),it is
>>     showing error:
>>
>>     Group DPPC not found in indexfile.
>>     Maybe you have non-default goups in your mdp file, while not using
>>     the '-n' option of grompp.
>>     In that case use the '-n' option.
>>
>>     To troubleshoot the error,I have kept one more group in index.ndx
>>     file with number of atoms which I found from dppc.itp file(at the
>>     end of file) like this
>>
>>     [DPPC]
>>     1    2    3    4    5    6    7    8    9   10   11   12   13  
>>     14   15
>>     16   17   18   19   20   21   22   23   24   25   26   27   28  
>>     29   30
>>     31   32   33   34   35   36   37   38   39   40   41   42   43  
>>     44   45
>>     46   47   48   49   50
> 
>     These numbers have to reference the atom numbers in the coordinate
>     file, not the [moleculetype]. Since you've done the latter, you get
>     the problem with T-coupling groups. But go back and use a coordinate
>     file that actually has DPPC in it.
> 
>     Mark
> 
> 
>>
>>     Again after running the grompp command (grompp -f nvt.mdp -c
>>     em.gro -p topol.top -n index.ndx -o nvt.tpr),I am getting the
>>     following error:
>>
>>     Atom 1 in multiple T-Coupling groups (1 and 2).
>>
>>     Please suggest me the reason as well as solution for this problem.
>>
>>
> 
> 
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-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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